Rangewide tidewater goby occupancy survey using environmental DNA

Abstract

Rangewide monitoring of fish species is critical for determining status and trends in distribution; however, implementations of large-scale distribution surveys have generally been constrained by time and cost. This study used environmental DNA (eDNA) to monitor the presence or absence of two endangered tidewater goby species, the northern tidewater goby (Eucyclogobius newberryi) and the southern tidewater goby (Eucyclogobius kristinae), across their combined geographic range that encompasses the entire California coast (1350 km). A total of 197 estuary sites were surveyed in coastal California from Del Norte to San Diego counties between May and September 2016. Among the 197 sites, a total of 430 water samples were collected (one to six per site), filtered, and tested for the presence/absence of northern and southern tidewater goby, using species-specific quantitative PCR assays. Northern tidewater goby were detected at 81 out of 175 sites and southern tidewater goby were detected at 4 out of 22 sites, resulting in a combined naive occupancy of 0.43. In contrast, application of a multi-scale occupancy model that accounted for imperfect detection estimated site occupancy at 0.55 (95% CRI 0.46–0.64), indicating that tidewater goby were present but not detected at 23 additional sites. This study illustrates that eDNA methods represent a reliable and efficient tool for aquatic species monitoring, but highlight the importance of accounting for imperfect detection by use of occupancy models in eDNA surveys. The tidewater goby eDNA distributional snapshot represents a baseline for evaluation of future trends in site occupancy that will inform conservation and management of this endangered species.